Down syndrome, caused by trisomy of human chromosome 21 (HSA21), is the most common autosomal form of mental retardation. The first report describing an association between Down syndrome (DS) and leukemia, which are an important cause of morbidity and mortality worldwide, was presented in 1930. Since that time, the increased incidence of acute leukemia in patients with DS has been clearly established. However, the M7 subtype, AMKL, acute megakaryoblastic leukemia has been found to be common in DS but relatively rare in non-DS. An instability in the control of bone marrow proliferation has been hypothesized as a predisposing factor. The incidence of acute myelogenous leukemia patients with DS has been noted by some to be similar to that in children without mongolism. Chromosome 21 is a model for the study of human chromosomal aneuploidy, and the construction of its physical and transcriptional maps is a necessary step in understanding the molecular basis of aneuploidy-dependent phenotypes.
Human chromosome 21 has a nearly complete physical map with a well-characterized contiguous set of overlapping YACs spanning most of its length (Chumakov et al., 1992; Shimizu et al., 1995; Korenberg et al., 1995). The demand for sequence-ready contigs and clones for gene isolation efforts has prompted the construction of numerous higher resolution contigs in cosmids (Patil et al., 1994; Soeda et al., 1995) and, more recently, in P1-derived artificial chromosomes (PACs; Oegawa et al. 1996 and Hubert et al. (1997) Genomics 41:218–226). Considerable mapping efforts exist in the region from CBR to D21S55 due to the common duplication of the region in partially trisomic individuals with several phenotypic features of DS, including mental retardation. However, the distal and adjacent, 4- to 5-Mb D21S55 to MX1 region is also associated with DS-CHD as well as other characteristic features of DS (Korenberg et al., 1992, 1994).
Although full monosomy of chromosome 21 is usually lethal in utero, there are rare cases of individuals with chromosome 21 deletions who survive. These individuals exhibit a characteristic subset of clinical features including psychomotor and growth retardation, congenital heart disease, holoprosencephaly, microphthalmia, skeletal malformations, and genital hypoplasia. Megakaryocytic abnormalities is added to this set and define a minimal “overlap” region for this feature through the clinical, cytogenetic, and molecular analysis of four patients with overlapping deletions of chromosome 21 and thrombocytopenia.
Nonchimeric YACs span this interval with a few gaps but higher resolution physical maps are not available for most of the D21S55 to MX1 region. DEL21RW carries two interstitial deletions, one in 21q21.3–22.1 defined by YAC 62G5 through YAC 760H5, and the second in 21q22.2, deleting IFNAR through CBR. DEL21LS carries an interstitial deletion of 21q22.1 from YAC 760H5 through the AML1 gene. Korenberg et al. reported that the deletion of patient DEL21HJ includes D21S93 through AML1. DEL21SV has a possible terminal deletion, 21q22.13-qter, extending from just proximal to D21S324 through D21S123. The common deleted region, or overlap region, is therefore from D21S324 through AML1, a region of less than 2 Mb that contains only three known genes, AML1, KCNE1, and UNO2. Bone marrow examination of two of the patients, DEL21HJ and Del 21RW, showed normocellular marrow with normal myelopoiesis, normal erythropoiesis, and small, dysplastic megakaryocytes with hypolobated nuclei. These two patients have decreased platelet activation by agonists with normal platelet ultrastructures. All four patients have platelet dysfunction characterized by low platelet counts in the range of 31–113×109/L. Further, all four subjects with chromosome 21 deletions that do not include this region have normal number of platelets.
A 3′ fragment of SH3P17 gene was found in a study to isolate SH3 domain containing genes (Sparks et al. 1996, Nature Biotechnology 14:741). This was mapped to 21 or large sub-region of 21 by a number of groups by using database matches to the published sequence. Katsanis N, et al (Hum Genet 1997 September; 100(34):477480) utilized information generated by various EST sequencing projects to enrich the transcription map of chromosome 21 and report the mapping of SH3P17 to 21q22.1 and the localisation of two genes previously mapped to HSA21 by Nagase and colleagues, KIAA0136 and KIAA0179 to 21q22.2 and 21q22.3 respectively. Chen H, and Antonarakis SE (Cytogenet Cell Genet 1997;78(34):213–215) identified portions of genes on human chromosome 21 and mapped the gene to YACs and cosmids within 21q22.1—>q22.2 between DNA markers D21S319 and D21S65 using hybridization and PCR amplification. Lastly, Guipponi et. al. 1998, Genomics 53:369–376 reported that they identified two isoforms of the human homolog of Xenopus Intersectin (ITSN) produced from alternate transcripts, the first of which, a short transcript is reportedly ubiquitously expressed, while the second longer transcript is exclusively expressed in brain tissue. Later, Guipponi et. al. 1998 Cytogenet Cell Genet. 83:218–220 reported that they had identified the genomic structure, sequence and precise mapping of the human intersectin gene and speculated that it may play a role in the determination of certain of the phenotypic characteristics of Down syndrome. The authors did not present evidence and corresponding observations or speculation regarding the role of the discovered genes apart from a possible relation to Down syndrome, and as such, are distinguishable from the research and discoveries embodied in the present invention.
The present invention provides the complete nucleotide sequence of several SH3 genes, including the SH3D1A gene and clones thereof, their association with platelet dysfunction and leukemia, including a part of the increased risk of leukemia seen in Down Syndrome, and with dysfunctions associated with neural development and particularly development in the CNS.